The CSV file of the GPS data set is here. Go here if you want to copy and paste this CSV file to your computer.
There are 1841 coordinates in this file from 1839 unique cases (i.e. 22 % of the total number of cases, 8288, reported in PACS). By year, the GPS data split like this:
Registered S3 method overwritten by 'cli':
method from
print.boxx spatstat
# A tibble: 8 x 4
year n gps perc
<dbl> <int> <int> <dbl>
1 2012 511 93 18.2
2 2013 2216 595 26.9
3 2014 130 5 3.85
4 2015 570 122 21.4
5 2016 1291 280 21.7
6 2017 2170 603 27.8
7 2018 835 60 7.19
8 NA 565 81 14.3
Considering only confirmed cases, it looks like:
# A tibble: 8 x 4
year n gps perc
<dbl> <int> <int> <dbl>
1 2012 203 93 45.8
2 2013 1248 573 45.9
3 2014 16 5 31.2
4 2015 267 122 45.7
5 2016 250 137 54.8
6 2017 1323 586 44.3
7 2018 317 60 18.9
8 NA 134 24 17.9
The duplicates are
# A tibble: 4 x 4
id source longitude latitude
<int> <chr> <dbl> <dbl>
1 7681 server 103. 18.0
2 7681 server 103. 18.1
3 6060 whatsapp 103. 18.1
4 6060 whatsapp 103. 18.0
There are 81 geocoded cases for which we don’t have any date:
# A tibble: 81 x 5
id onset hospitalization consultation sample_collection
<int> <date> <date> <date> <date>
1 937 NA NA NA NA
2 941 NA NA NA NA
3 1112 NA NA NA NA
4 1211 NA NA NA NA
5 1281 NA NA NA NA
6 1282 NA NA NA NA
7 1286 NA NA NA NA
8 1489 NA NA NA NA
9 1572 NA NA NA NA
10 1869 NA NA NA NA
# … with 71 more rows
The CSV file of these cases is here. Go here if you want to copy and paste this CSV file to your computer. The split by source reads
# A tibble: 4 x 2
source n
<chr> <int>
1 new_gps 821
2 old_gps 736
3 server 31
4 whatsapp 253
The split of data according to the test and the availability of GPS coordinates is:
test
gps negative not tested positive
FALSE 1491 2800 2158
TRUE 7 232 1600
The cases with GPS data and reported as negative are:
[1] 2218 2303 2375 2423 4925 5052 7097
Here is a map of the geolocated cases:
The blue crosses are the Vayakorn Inn and the Institut Pasteur du Laos. Same with satellite image background: